Multiple platform build/check report for BioC 3.6 - CHECK report for FlowRepositoryR on tokay1

Package: FlowRepositoryR

Version: 1.10.0

Command: rm -rf FlowRepositoryR.buildbin-libdir FlowRepositoryR.Rcheck && mkdir FlowRepositoryR.buildbin-libdir FlowRepositoryR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=FlowRepositoryR.buildbin-libdir FlowRepositoryR_1.10.0.tar.gz >FlowRepositoryR.Rcheck\00install.out 2>&1 && cp FlowRepositoryR.Rcheck\00install.out FlowRepositoryR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=FlowRepositoryR.buildbin-libdir --install="check:FlowRepositoryR-install.out" --force-multiarch --no-vignettes --timings FlowRepositoryR_1.10.0.tar.gz

StartedAt: 2018-04-12 00:02:48 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:03:54 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 66.0 seconds

RetCode: 0

Status: OK

CheckDir: FlowRepositoryR.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf FlowRepositoryR.buildbin-libdir FlowRepositoryR.Rcheck && mkdir FlowRepositoryR.buildbin-libdir FlowRepositoryR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=FlowRepositoryR.buildbin-libdir FlowRepositoryR_1.10.0.tar.gz >FlowRepositoryR.Rcheck\00install.out 2>&1 && cp FlowRepositoryR.Rcheck\00install.out FlowRepositoryR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=FlowRepositoryR.buildbin-libdir --install="check:FlowRepositoryR-install.out" --force-multiarch --no-vignettes --timings FlowRepositoryR_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/FlowRepositoryR.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'FlowRepositoryR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FlowRepositoryR' version '1.10.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'FlowRepositoryR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
attachmentProxy: no visible global function definition for 'new'
fcsProxy: no visible global function definition for 'new'
flowRep.search: no visible global function definition for 'is'
flowRepData: no visible global function definition for 'new'
flowRepOrganization: no visible global function definition for 'new'
attachments<-,flowRepData: no visible global function definition for
  'is'
fcs.files<-,flowRepData: no visible global function definition for 'is'
impc.experiments<-,flowRepData: no visible global function definition
  for 'is'
Undefined global functions or variables:
  is new
Consider adding
  importFrom("methods", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/FlowRepositoryR.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'FlowRepositoryR' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'FlowRepositoryR'
    finding HTML links ... done
    FlowRepositoryR-package                 html  
    attachmentProxy-class                   html  
    download-methods                        html  
    fcsProxy-class                          html  
    fileProxy-class                         html  
    flowRep.get                             html  
    flowRep.ls                              html  
    flowRep.search                          html  
    flowRep.submitGeneStatus                html  
    flowRep.submitImpcResults               html  
    flowRepData-class                       html  
    flowRepOrganization-class               html  
    forgetFlowRepositoryCredentials         html  
    getFlowRepositoryURL                    html  
    id-methods                              html  
    ilarCodeDescription                     html  
    impcCodeDescription                     html  
    impcResultsCopy-methods                 html  
    is.downloaded-methods                   html  
    listKnownIlarCodes                      html  
    setFlowRepositoryCredentials            html  
    setFlowRepositoryURL                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'FlowRepositoryR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FlowRepositoryR' as FlowRepositoryR_1.10.0.zip
* DONE (FlowRepositoryR)
In R CMD INSTALL
In R CMD INSTALL


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("FlowRepositoryR")
File about.txt downloaded.
File GvHD2.fcs downloaded.
Downloading to C:/Users/biocbuild/bbs-3.6-bioc/meat/FlowRepositoryR.Rcheck/tests_i386/FR-FCM-ZZJ7 
File GvHD2.fcs is downloaded already.
File GvHD8.fcs downloaded.
File about.txt is downloaded already.
File ExampleGate.png downloaded.
Download finished.
Loading required package: bitops


RUNIT TEST PROTOCOL -- Thu Apr 12 00:03:42 2018 
*********************************************** 
Number of test functions: 16 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
FlowRepositoryR RUnit Tests - 16 test functions, 0 errors, 0 failures
Number of test functions: 16 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   2.01    0.15    5.20


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("FlowRepositoryR")
File about.txt downloaded.
File GvHD2.fcs downloaded.
Downloading to C:/Users/biocbuild/bbs-3.6-bioc/meat/FlowRepositoryR.Rcheck/tests_x64/FR-FCM-ZZJ7 
File GvHD2.fcs is downloaded already.
File GvHD8.fcs downloaded.
File about.txt is downloaded already.
File ExampleGate.png downloaded.
Download finished.
Loading required package: bitops


RUNIT TEST PROTOCOL -- Thu Apr 12 00:03:49 2018 
*********************************************** 
Number of test functions: 16 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
FlowRepositoryR RUnit Tests - 16 test functions, 0 errors, 0 failures
Number of test functions: 16 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   3.45    0.20    6.67

name	user	system	elapsed
attachmentProxy-class	0.18	0.06	0.50
download-methods	0.22	0.00	1.98
fcsProxy-class	0.01	0.00	0.25
fileProxy-class	0.02	0.00	0.25
flowRep.get	0.01	0.00	0.25
flowRep.ls	0.00	0.00	0.27
flowRep.search	0.02	0.00	0.25
flowRep.submitGeneStatus	0	0	0
flowRep.submitImpcResults	0	0	0
flowRepData-class	0.02	0.00	0.23
flowRepOrganization-class	0.01	0.00	0.25
forgetFlowRepositoryCredentials	0	0	0
getFlowRepositoryURL	0	0	0
id-methods	0.04	0.00	0.27
ilarCodeDescription	0	0	0
impcCodeDescription	0	0	0
impcResultsCopy-methods	0.01	0.00	0.25
is.downloaded-methods	0.05	0.01	0.26
listKnownIlarCodes	0	0	0
setFlowRepositoryCredentials	0	0	0
setFlowRepositoryURL	0	0	0

name	user	system	elapsed
attachmentProxy-class	0.22	0.06	0.54
download-methods	0.56	0.00	2.41
fcsProxy-class	0.06	0.00	0.27
fileProxy-class	0.03	0.01	0.26
flowRep.get	0.05	0.00	0.25
flowRep.ls	0.03	0.00	0.30
flowRep.search	0.00	0.00	0.28
flowRep.submitGeneStatus	0	0	0
flowRep.submitImpcResults	0.02	0.00	0.01
flowRepData-class	0.03	0.00	0.25
flowRepOrganization-class	0.02	0.00	0.25
forgetFlowRepositoryCredentials	0	0	0
getFlowRepositoryURL	0	0	0
id-methods	0.06	0.00	0.28
ilarCodeDescription	0	0	0
impcCodeDescription	0	0	0
impcResultsCopy-methods	0.03	0.00	0.27
is.downloaded-methods	0.06	0.00	0.28
listKnownIlarCodes	0	0	0
setFlowRepositoryCredentials	0	0	0
setFlowRepositoryURL	0	0	0

CHECK report for FlowRepositoryR on tokay1

Summary

Command output

Installation output

Tests output

Example timings